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» Functional annotation of regulatory pathways
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BMCBI
2007
165views more  BMCBI 2007»
13 years 7 months ago
Automatic reconstruction of a bacterial regulatory network using Natural Language Processing
Background: Manual curation of biological databases, an expensive and labor-intensive process, is essential for high quality integrated data. In this paper we report the implement...
Carlos Rodríguez Penagos, Heladia Salgado, ...
BMCBI
2010
129views more  BMCBI 2010»
13 years 7 months ago
Uncovering packaging features of co-regulated modules based on human protein interaction and transcriptional regulatory networks
Background: Network co-regulated modules are believed to have the functionality of packaging multiple biological entities, and can thus be assumed to coordinate many biological fu...
Lina Chen, Hong Wang, Liangcai Zhang, Wan Li, Qian...
RECOMB
2010
Springer
13 years 9 months ago
Algorithms for Detecting Significantly Mutated Pathways in Cancer
Abstract. Recent genome sequencing studies have shown that the somatic mutations that drive cancer development are distributed across a large number of genes. This mutational heter...
Fabio Vandin, Eli Upfal, Benjamin J. Raphael
APBC
2004
122views Bioinformatics» more  APBC 2004»
13 years 8 months ago
Integrating Biopathway Databases for Large-scale Modeling and Simulation
Biopathway databases have been developed, such as KEGG and EcoCyc, that compile interaction structures of biopathways together with biological annotations. However, these biopathw...
Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, Sato...
BMCBI
2010
106views more  BMCBI 2010»
13 years 7 months ago
A computational evaluation of over-representation of regulatory motifs in the promoter regions of differentially expressed genes
Background: Observed co-expression of a group of genes is frequently attributed to co-regulation by shared transcription factors. This assumption has led to the hypothesis that pr...
Guofeng Meng, Axel Mosig, Martin Vingron